SRM methods in Alzheimer's disease and neurological disease assays

1. A multiplexed LC-SRM-MS assay for the measurement of a plurality of Alzheimer's disease associated proteins in a single sample comprising:

a) generating a set of optimal peptides and corresponding transitions for each protein monitored;

b) optimizing the collision energy for each transition such that interference among the transitions monitored is avoided;

c) selecting a set of transitions that have the greatest peak areas are monitored for each of the proteins, and wherein the selected transitions do not interfere with the ions in the sample;

d) monitoring the detected set of transitions for each protein in the sample, there by measuring a plurality of proteins in the sample.

2. The assay of claim 1 , wherein each monitored peptide

(i) has a monoisotopic mass of 700-5000 Da; and

(ii) does not contain a cysteine or a methionine.

3. The assay of claim 1 , wherein the transitions for each peptide

(i) have one of the four most intense b or y transition ions;

(ii) has m/z values of at least 30 m/z above or below those of a precursor ion;

(iii) do not interfere with transitions from other peptides; and

(iv) represent transitions due to breakage of peptide bond at different sites of the protein.

4. The assay according to claim 1 , wherein the peptides do not include any peptide that is bounded by KK, KR, RK or RR, either upstream or downstream in the corresponding protein sequence.

5. The assay according to claim 1 , wherein each peptide of said set of peptides is unique to the corresponding protein.

6. The assay according to claim 1 , wherein the peptides do not include peptides which were observed in post-translational modified forms.

7. The assay according to claim 1 , wherein each set of peptides is prioritized according to one or more of the following ordered set of criteria:

(a) unique peptides first, then non-unique;

(b) peptides with no observed post-translational modifications first, then those observed with post-translational modifications;

(c) peptides within the mass range 800-3500 Da first, then those outside of 800-3500 Da; and

(d) sorted by decreasing number of variant residues.

8. The assay according to claim 7 , wherein each set of peptides is prioritized according to all of the ordered set of criteria.

9. The assay according to claim 1 , wherein each prioritized set of peptides contains 1-5 peptides.

10. The assay according to claim 1 , wherein the two best peptides per protein and the two best transitions per peptide are selected based on experimental data resulting from LC-SRM-MS analysis of one or more of the following experimental samples: a biological disease sample, a biological control sample, and a mixture of synthetic peptides of interest.

11. The assay according to claim 10 , wherein the biological disease and biological control samples are processed using an immunodepletion method prior to LC-SRM-MS analysis.

12. The assay according to claim 11 , wherein the experimental samples contain internal standard peptides.

13. The assay according to claim 11 , wherein the LC-SRM-MS analysis method specifies a maximum of 7000 transitions, including transitions of the internal standard peptides and transitions.

14. The assay according to claim 1 , wherein the top two transitions per peptide are selected according to one or more of the following criteria:

(1) the transitions exhibit the largest peak areas measured in either of the two biological experimental samples;

(2) the transitions are not interfered with by other ions;

(3) the transitions do not exhibit an elution profile that visually differs from those of other transitions of the same peptide;

(4) the transitions are not beyond the detection limit of both of the two biological experimental samples; and

(5) the transitions do not exhibit interferences.

15. The assay according to claim 1 , wherein the top two peptides per protein are selected according to one or more of the following criteria:

(1) one or more peptides exhibit two transitions according to claim 12 and represent the largest combined peak areas of the two transitions according to claim 12 ; and

(2) one or more peptides exhibit one transition according to claim 12 and represent the largest combined peak areas of the two transitions according to claim 12 .

16. A diagnostic assay developed according to the method of claim 1 .